Mercurial > repos > avowinkel > picard
comparison picard_AddOrReplaceReadGroups.xml @ 0:5166ed57b1c4 draft
Uploaded version 1.135
author | avowinkel |
---|---|
date | Mon, 06 Jul 2015 14:46:32 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:5166ed57b1c4 |
---|---|
1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="1.135-gx-1"> | |
2 <description>add or replaces read group information</description> | |
3 <macros> | |
4 <import>picard_macros.xml</import> | |
5 <import>read_group_macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <command> | |
9 @define_read_group_helpers@ | |
10 #set $rg_auto_name = $read_group_name_default($inputFile) | |
11 @set_read_group_vars@ | |
12 @java_options@ | |
13 java -jar \$JAVA_JAR_PATH/picard.jar | |
14 AddOrReplaceReadGroups | |
15 INPUT="${inputFile}" | |
16 $format_read_group("RGLB=", $rg_lb, '"') | |
17 $format_read_group("RGPL=", $rg_pl, '"') | |
18 $format_read_group("RGPU=", $rg_pu, '"') | |
19 $format_read_group("RGSM=", $rg_sm, '"') | |
20 $format_read_group("RGID=", $rg_id, '"') | |
21 $format_read_group("RGDS=", $rg_ds, '"') | |
22 $format_read_group("RGPI=", $rg_pi, '"') | |
23 $format_read_group("RGDT=", $rg_dt, '"') | |
24 VALIDATION_STRINGENCY="${validation_stringency}" | |
25 QUIET=true | |
26 VERBOSITY=ERROR | |
27 OUTPUT="${outFile}" | |
28 | |
29 </command> | |
30 | |
31 <inputs> | |
32 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> | |
33 <expand macro="read_group_inputs_picard" /> | |
34 <expand macro="VS" /> | |
35 | |
36 </inputs> | |
37 | |
38 <outputs> | |
39 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/> | |
40 </outputs> | |
41 | |
42 <stdio> | |
43 <exit_code range="1:" level="fatal"/> | |
44 </stdio> | |
45 | |
46 <tests> | |
47 <test> | |
48 <param name="inputFile" value="picard_ARRG.bam" /> | |
49 <param name="LB" value="tumor-a" /> | |
50 <param name="PL" value="ILLUMINA" /> | |
51 <param name="PU" value="run-1" /> | |
52 <param name="SM" value="sample-a" /> | |
53 <param name="ID" value="id-1" /> | |
54 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" /> | |
55 </test> | |
56 </tests> | |
57 <help> | |
58 | |
59 .. class:: infomark | |
60 | |
61 **Purpose** | |
62 | |
63 Add or Replace Read Groups in an input BAM or SAM file. | |
64 | |
65 @dataset_collections@ | |
66 | |
67 @RG@ | |
68 | |
69 @description@ | |
70 | |
71 INPUT=File | |
72 I=File Input file (bam or sam). Required. | |
73 | |
74 OUTPUT=File | |
75 O=File Output file (bam or sam). Required. | |
76 | |
77 SORT_ORDER=SortOrder | |
78 SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT. | |
79 Default value: null. Possible values: {unsorted, queryname, coordinate} | |
80 | |
81 RGID=String | |
82 ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default | |
83 value. | |
84 | |
85 RGLB=String | |
86 LB=String Read Group Library Required. | |
87 | |
88 RGPL=String | |
89 PL=String Read Group platform (e.g. illumina, solid) Required. | |
90 | |
91 RGPU=String | |
92 PU=String Read Group platform unit (eg. run barcode) Required. | |
93 | |
94 RGSM=String | |
95 SM=String Read Group sample name Required. | |
96 | |
97 RGCN=String | |
98 CN=String Read Group sequencing center name Default value: null. | |
99 | |
100 RGDS=String | |
101 DS=String Read Group description Default value: null. | |
102 | |
103 RGDT=Iso8601Date | |
104 DT=Iso8601Date Read Group run date Default value: null. | |
105 | |
106 RGPI=Integer | |
107 PI=Integer Read Group predicted insert size Default value: null. | |
108 | |
109 @more_info@ | |
110 </help> | |
111 </tool> | |
112 | |
113 | |
114 | |
115 | |
116 | |
117 | |
118 | |
119 | |
120 | |
121 | |
122 | |
123 | |
124 | |
125 |